{% load static %}
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
    "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<html lang="en" xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
<head>
  <meta name="generator" content="HTML Tidy for Mac OS X (vers 31 October 2006 - Apple Inc. build 13), see www.w3.org" />

  <title>Peptide Prediction</title>
  <meta http-equiv="Content-Type" content="text/html; charset=us-ascii" />
  <link rel="stylesheet" href="{% static 'css/stylesheet.css' %}" type="text/css" />
    <script src="{% static 'js/sms_common.js' %}"></script>
    <script src="{% static 'js/jquery-3.4.1.min.js' %}"></script>
    <script src="{% static 'js/sms_genetic_codes.js' %}"></script>
    <script src="{% static 'js/peptide_predict.js' %}"></script>
</head>

<body class="main" onload="document.main_form.main_submit.focus()">
  <!-- MAIN TABLE -->

  <table border="0" cellspacing="2" cellpadding="2">
    <tbody>
      <tr>

        <td class="program">
          <table border="0" cellspacing="0" cellpadding="2">
            <tbody>
              <tr>
                <td class="sms">Peptide Prediction</td>
              </tr>



              <tr>
                <td class="description">
                  ORF Finder searches for open reading frames (ORFs) in the DNA sequence you enter. The program returns the range of each ORF, along with its protein translation. Use ORF Finder to search newly sequenced DNA for potential protein encoding segments. ORF Finder supports the entire IUPAC alphabet and several genetic codes.<br />
                  <br />

                  <form action="predict_peptide" method="post" name="main_form" id="main_form">
                    Paste the text into the text area below. Input limit is 100,000,000 characters.<br />
                    <textarea rows="10" cols="100" name="fastas">
>1
ATGCCCTTTGACAGGCAGAAAATCGTGGAAGCGGTGAAGGAGGCTAAAGCCCGGGCCAAG
CCGCGTAACTTCACACAGAGTGTCGAAGTTGCAGTGAACCTCAAGGATATCGACCTAAAA
CGTCCCGAAAATAGGTTTAAACTCGAGGTTGTCCTTCCTCACGGGAGAGGCAAAGATGTG
AAGATCGCGGTCATCGCTGATGGTGCAGTTGCCGAGGCGGCGAGGAGGCTCGGGCTTGAT
GTTATTAGTAGTGCCGAGTTGGAGGAGATAGCTCAAAGCCCTAGACAGGCGAGAAAGTTG
GCTAAGAAGTACGACTTCTTCATAGCTGAAGCCCCATTAATGCCAAAGATAGGTAGGTAC
CTGGGTAAGTACTTGGGTCCCAGGAACAAGATGCCAGTCGTCGTTCCTCCAACGATGAGT
AACTTAGAACCCATAGTTGAGAAGCTCAAGAAGACGGTAAGGATACAGCTAAAGAACAAC
CCAGTGGTCCATGCCCCAGTTGGAACCGAAAAGATGAGCGACGAGGAGATAGCGGAGAAC
ATTGAAACGGTGCTGAACGCTATAATAGGTAAGCTCGAGAGGGGAGAGAGCCAGATAAAG
TCAGTGTACGTTAAGACCACGATGGGTCCAGCCGTTAAAGTGAAGGGGTAG
</textarea><br />

                    <input type="button" value="Submit" name="main_submit" onclick="try{orfFind(document)} catch(e) {alert('The following error was encountered: ' + e);}" />
                      <input type="button" value="Clear" onclick="document.forms[0].elements[0].value = ' '" />
                      <input type="reset" value="Reset" />

                    <ul>
                      <li>ORFs can begin with: <select name="start">
                        <option selected="selected" value="any">
                          any codon
                        </option>

                        <option value="a[tu]g">
                          atg
                        </option>

                        <option value="a[tu]g|g[tu]g|c[tu]g|[tu][tu]g">
                          atg, gtg, ctg, ttg
                        </option>
                      </select> .</li>

                      <li>Search for ORFs in reading frame <select name="position">
                        <option selected="selected" value="0">
                          1
                        </option>

                        <option value="1">
                          2
                        </option>

                        <option value="2">
                          3
                        </option>

                        <option value="all">
                          1, 2, and 3
                        </option>
                      </select> on the <select name="strand">
                        <option selected="selected" value="direct">
                          direct
                        </option>

                        <option value="reverse">
                          reverse
                        </option>
                          <option value="any chain">
                          any chain
                        </option>
                      </select> strand.</li>

                      <li>Only return ORFs that are at least <input type="text" value="30" name="least_length"/>codons long.</li>

                      <li>Use the <select name="genetic_code">
                        <option selected="selected" value="transl_table=1">
                          standard (1)
                        </option>

                        <option value="transl_table=2">
                          vertebrate mitochondrial (2)
                        </option>

                        <option value="transl_table=3">
                          yeast mitochondrial (3)
                        </option>

                        <option value="transl_table=4">
                          mold mitochondrial (4)
                        </option>

                        <option value="transl_table=5">
                          invertebrate mitochondrial (5)
                        </option>

                        <option value="transl_table=6">
                          ciliate nuclear (6)
                        </option>

                        <option value="transl_table=9">
                          echinoderm mitochondrial (9)
                        </option>

                        <option value="transl_table=10">
                          euplotid nuclear (10)
                        </option>

                        <option value="transl_table=11">
                          bacterial (11)
                        </option>

                        <option value="transl_table=12">
                          alternative yeast nuclear (12)
                        </option>

                        <option value="transl_table=13">
                          ascidian mitochondrial (13)
                        </option>

                        <option value="transl_table=14">
                          flatworm mitochondrial (14)
                        </option>

                        <option value="transl_table=15">
                          Blepharisma macronuclear (15)
                        </option>

                        <option value="transl_table=16">
                          chlorophycean mitochondrial (16)
                        </option>

                        <option value="transl_table=21">
                          trematode mitochondrial (21)
                        </option>

                        <option value="transl_table=22">
                          Scenedesmus obliquus mitochondrial (22)
                        </option>

                        <option value="transl_table=23">
                          Thraustochytrium mitochondrial (23)
                        </option>
                      </select> <a href="genetic_code">genetic code</a>.</li>
                    </ul>
                  </form>
                </td>
              </tr>


            </tbody>
          </table><!-- MAIN TABLE END -->
        </td>
      </tr>
    </tbody>
  </table>
</body>
</html>
